SEGUL

An ultrafast and mobile-friendly genomic toolkit.

Simplify tedious, complex, and error-prone tasks in exploring, cleaning, and shaping large genomic datasets. SEGUL is free, open-source, and cross-platform.

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SEGUL

News

SEGUL v0.25.0 is here

Terminal viewers, charts, and a much faster read summary. The redesigned SEGUI v1.2.0 is out on Google Play and rolling out to other stores.

What's new in v0.25.0 →
SEGUI on Android showing per-base read quality for a Bunomys sample
Read quality in SEGUI v1.2.0 on Android, from 921 MB of raw reads.

From raw reads to alignment supermatrix

Prepare large genomic datasets efficiently in one place

Redesigned interface · SEGUI v1.2.0

9 tools →

Alignments

Multi-locus alignment matrices

Concatenate Convert Compute genetic distances Filter Convert partition Split Summarize Trim Unalign
8 tools →

Sequences

Samples and IDs inside alignments

Add Extract Extract and map Filter Remove Rename Translate Transpose
4 tools →

Genomics

Raw reads and assemblies

Summarize reads Summarize contigs Convert MAF Summarize MAF
~/phylogenomics

# Concatenate 4,000 loci into a supermatrix

$ segul align concat -d loci/ --output supermatrix --part raxml

# Keep loci with at least 75% taxon coverage

$ segul align filter -d loci/ --percent 0.75

# Summarize raw reads

$ segul read summary -d raw_reads/

$

File formats

Support for various sequence formats.

  • FASTA

    Alignments, contigs

    .fasta .fa .fas

  • NEXUS

    Alignments

    .nex .nexus

  • PHYLIP

    Relaxed alignments

    .phy .phylip

  • FASTQ.gz

    Raw reads

    .fastq .fq

  • MAF.gz

    Genome alignments

    .maf

  • BED.gz

    Loci

    .bed

  • Partitions

    RAxML, NEXUS

    .txt .nex

All supported extensions →

Built-in viewers

Inspect alignments and summaries in the app or the terminal.

Check thousands of loci and their summary statistics without leaving SEGUL. The app and the command line show the same views.

SEGUI · Linux
SEGUI alignment viewer on Linux showing 49 shrew taxa of a UCE locus with colored bases
SEGUI alignment viewer. Point and click through loci. Guide →
$ segul view align --input uce-10.nex
segul view align in a terminal showing the same UCE locus with colored bases
segul view align. The same viewer in the terminal. Guide →
SEGUI · Linux
SEGUI alignment summary report showing a histogram of locus length across 4,040 loci
SEGUI summary report. Charts and tables of a summary run. Guide →
$ segul view summary --input alignment-report.json
segul view summary in a terminal showing a histogram of sites per locus across 4,040 loci
segul view summary. The same report as terminal plots. Guide →

Data: 4,040 UCE loci from 102 shrew samples, Esselstyn et al. 2021.

Easy to use

A guided graphical app and a concise command line, backed by documentation for every feature.

Accessible and reproducible

Runs on phones, laptops, and clusters with no runtime dependencies, Docker, or Singularity.

Fast and memory efficient

Written in Rust and parallel by default, making it simple to use, fast and memory efficient.

Interfaces

Different ways to interact with SEGUL.

GUI

SEGUI app

Point-and-click tools for desktop, tablet, and phone. Install from your platform's app store.

Installation guide →

CLI

Command line

Script thousands of loci in a pipeline. Install from Bioconda, cargo, or a pre-built binary.

$ conda install bioconda::segul
Installation guide →

API

Python, Rust, and R

Call SEGUL from your own code with pysegul or the segul crate.

$ pip install pysegul
Installation guide →

Install SEGUL GUI, free.

Desktop, tablet, and phone. Looking for the command line? See every install option.

Get it fromMicrosoft StoreDownload on theApp StoreGet it onGoogle PlayGet it from theSnap Store

Handika, H., and J. A. Esselstyn. 2024. SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets. Molecular Ecology Resources, 24(7).https://doi.org/10.1111/1755-0998.13964